# electronic Ligand Builder and Optimisation Workbench (eLBOW)
#   - a module of PHENIX version dev-svn-
#   - file written: Sun May 24 08:42:52 2020
#   Inital geometry file: a 145 line input string
#   Ligand name: O-(2-bromophenyl)-N-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbonyl]-D-tyrosine
#   Quantum optimisation: True
#   Method: PBEh-3c
#   Random seed: 3628800
#   SMILES string: OC(=O)[C@@H](Cc1ccc(Oc2ccccc2Br)cc1)NC(=O)C34CC5CC(CC(C5)C3)C4
#
data_comp_list
loop_
_chem_comp.id
_chem_comp.three_letter_code
_chem_comp.name
_chem_comp.group
_chem_comp.number_atoms_all
_chem_comp.number_atoms_nh
_chem_comp.desc_level
_chem_comp.initial_date
_chem_comp.modified_date
_chem_comp.source
 PH9  PH9  O-(2-bromophenyl)-N-[(3S,5S,7S)-tricyclo[3.3.1.1~3,7~]dec-1-ylcarbonyl]-D-tyrosine  ligand  60  32  .  2021-08-20  2021-08-20  
;
Directly from eLBOW using geometry from QM method PBEh-3c with CPCM solvent model
Validated by Mogul as GRAND
;

data_comp_PH9
loop_
_chem_comp_atom.comp_id
_chem_comp_atom.atom_id
_chem_comp_atom.type_symbol
_chem_comp_atom.type_energy
_chem_comp_atom.charge
_chem_comp_atom.partial_charge
_chem_comp_atom.x
_chem_comp_atom.y
_chem_comp_atom.z
 PH9  CB2   C   CR6   0   0.135  -10.5018  55.5787  47.7672
 PH9  CB3   C   CR16  0  -0.314  -11.3937  54.5460  48.0343
 PH9  CB4   C   CR16  0  -0.307  -12.5139  54.7422  48.8298
 PH9  CB6   C   CR6   0   0.334  -12.7514  55.9953  49.3698
 PH9  CB5   C   CR16  0  -0.306  -11.8808  57.0476  49.1143
 PH9  CB1   C   CR16  0  -0.282  -10.7681  56.8307  48.3175
 PH9  C2    C   CH1   0  -0.222   -7.9793  55.7507  47.6207
 PH9  C1    C   CH2   0  -0.519   -9.2870  55.3323  46.9139
 PH9  N     N   NH1   0  -0.627   -7.9401  55.2854  48.9749
 PH9  C     C   C     0   0.634   -7.8622  56.1139  50.0392
 PH9  CO2   C   C     0   0.553   -6.7716  55.2559  46.8450
 PH9  O     O   O     0  -0.482   -7.6425  57.3090  49.9114
 PH9  OC1   O   OH1   0  -0.592   -6.7513  55.7568  45.6176
 PH9  OC2   O   O     0  -0.424   -5.9419  54.4994  47.2759
 PH9  OAB   O   O2    0  -0.504  -13.8908  56.1544  50.1162
 PH9  CA1   C   CR6   0   0.382  -13.8663  57.0069  51.1749
 PH9  CA2   C   CR6   0  -0.203  -14.7906  58.0439  51.2331
 PH9  CA3   C   CR16  0  -0.235  -14.8307  58.8925  52.3317
 PH9  CA4   C   CR16  0  -0.256  -13.9285  58.7147  53.3690
 PH9  CA5   C   CR16  0  -0.255  -12.9971  57.6859  53.3119
 PH9  CA6   C   CR16  0  -0.308  -12.9674  56.8336  52.2209
 PH9  BRA2  BR  BR    0  -0.022  -15.9938  58.2880  49.8083
 PH9  CC4   C   CH2   0  -0.429   -9.6099  55.3048  53.9248
 PH9  CC3   C   CH1   0  -0.248   -8.1879  55.8636  53.8786
 PH9  CC5   C   CH1   0  -0.255   -9.7741  54.2524  52.8279
 PH9  CC2   C   CH2   0  -0.394   -7.9374  56.5048  52.5123
 PH9  CC6   C   CH2   0  -0.413   -9.5204  54.8882  51.4595
 PH9  CC1   C   CT    0  -0.271   -8.0896  55.4604  51.3983
 PH9  C10   C   CH2   0  -0.416   -8.7706  53.1189  53.0540
 PH9  CC8   C   CH1   0  -0.248   -7.3471  53.6798  53.0120
 PH9  CC9   C   CH2   0  -0.418   -7.1837  54.7334  54.1082
 PH9  CC7   C   CH2   0  -0.408   -7.0866  54.3166  51.6445
 PH9  HB3   H   HCR6  0   0.256  -11.2081  53.5595  47.6266
 PH9  HB4   H   HCR6  0   0.270  -13.1946  53.9250  49.0320
 PH9  HB5   H   HCR6  0   0.279  -12.0620  58.0335  49.5235
 PH9  HB1   H   HCR6  0   0.257  -10.0982  57.6620  48.1328
 PH9  H2    H   HCH1  0   0.302   -7.9263  56.8416  47.6450
 PH9  H11   H   HCH2  0   0.264   -9.2426  54.2711  46.6565
 PH9  H12   H   HCH2  0   0.277   -9.3655  55.8794  45.9727
 PH9  HN    H   HNH1  0   0.395   -8.1471  54.3121  49.1309
 PH9  HC1   H   HOH1  0   0.487   -5.9911  55.4095  45.1269
 PH9  HA3   H   HCR6  0   0.286  -15.5540  59.6954  52.3747
 PH9  HA4   H   HCR6  0   0.273  -13.9585  59.3792  54.2214
 PH9  HA5   H   HCR6  0   0.271  -12.2952  57.5417  54.1226
 PH9  HA6   H   HCR6  0   0.283  -12.2529  56.0204  52.1771
 PH9  HC42  H   HCH2  0   0.223  -10.3341  56.1156  53.7857
 PH9  HC3   H   HCH1  0   0.227   -8.0675  56.6257  54.6541
 PH9  HC5   H   HCH1  0   0.230  -10.7925  53.8511  52.8475
 PH9  HC21  H   HCH2  0   0.227   -8.6475  57.3215  52.3557
 PH9  HC22  H   HCH2  0   0.228   -6.9352  56.9421  52.4853
 PH9  HC61  H   HCH2  0   0.232   -9.6809  54.1396  50.6779
 PH9  HC62  H   HCH2  0   0.234  -10.2423  55.6892  51.2661
 PH9  H101  H   HCH2  0   0.227   -8.9557  52.6416  54.0213
 PH9  H102  H   HCH2  0   0.225   -8.8973  52.3450  52.2899
 PH9  HC8   H   HCH1  0   0.230   -6.6268  52.8711  53.1653
 PH9  HC91  H   HCH2  0   0.224   -6.1642  55.1319  54.0996
 PH9  HC92  H   HCH2  0   0.224   -7.3410  54.2809  55.0924
 PH9  HC71  H   HCH2  0   0.228   -7.1698  53.5485  50.8701
 PH9  HC72  H   HCH2  0   0.238   -6.0633  54.7019  51.5961
 PH9  HC41  H   HCH2  0   0.227   -9.8171  54.8673  54.9063

loop_
_chem_comp_bond.comp_id
_chem_comp_bond.atom_id_1
_chem_comp_bond.atom_id_2
_chem_comp_bond.type
_chem_comp_bond.value_dist
_chem_comp_bond.value_dist_esd
_chem_comp_bond.value_dist_neutron
 PH9  CB2  CB3   aromatic  1.390  0.020  1.390
 PH9  CB2  CB1   aromatic  1.393  0.020  1.393
 PH9  CB2  C1    single    1.505  0.020  1.505
 PH9  CB3  CB4   aromatic  1.388  0.020  1.388
 PH9  CB3  HB3   single    0.930  0.020  1.080
 PH9  CB4  CB6   aromatic  1.385  0.020  1.385
 PH9  CB4  HB4   single    0.930  0.020  1.080
 PH9  CB6  CB5   aromatic  1.389  0.020  1.389
 PH9  CB6  OAB   single    1.371  0.020  1.371
 PH9  CB5  CB1   aromatic  1.386  0.020  1.386
 PH9  CB5  HB5   single    0.930  0.020  1.080
 PH9  CB1  HB1   single    0.930  0.020  1.080
 PH9  C2   C1    single    1.544  0.020  1.544
 PH9  C2   N     single    1.432  0.020  1.432
 PH9  C2   CO2   single    1.518  0.020  1.518
 PH9  C2   H2    single    0.970  0.020  1.090
 PH9  C1   H11   single    0.970  0.020  1.090
 PH9  C1   H12   single    0.970  0.020  1.090
 PH9  N    C     single    1.351  0.020  1.351
 PH9  N    HN    single    0.860  0.020  1.020
 PH9  C    O     double    1.222  0.020  1.222
 PH9  C    CC1   single    1.525  0.020  1.525
 PH9  CO2  OC1   single    1.326  0.020  1.326
 PH9  CO2  OC2   double    1.203  0.020  1.203
 PH9  OC1  HC1   single    0.850  0.020  0.980
 PH9  OAB  CA1   single    1.359  0.020  1.359
 PH9  CA1  CA2   aromatic  1.390  0.020  1.390
 PH9  CA1  CA6   aromatic  1.390  0.020  1.390
 PH9  CA2  CA3   aromatic  1.389  0.020  1.389
 PH9  CA2  BRA2  single    1.881  0.020  1.881
 PH9  CA3  CA4   aromatic  1.386  0.020  1.386
 PH9  CA3  HA3   single    0.930  0.020  1.080
 PH9  CA4  CA5   aromatic  1.389  0.020  1.389
 PH9  CA4  HA4   single    0.930  0.020  1.080
 PH9  CA5  CA6   aromatic  1.385  0.020  1.385
 PH9  CA5  HA5   single    0.930  0.020  1.080
 PH9  CA6  HA6   single    0.930  0.020  1.080
 PH9  CC4  CC3   single    1.528  0.020  1.528
 PH9  CC4  CC5   single    1.529  0.020  1.529
 PH9  CC4  HC41  single    0.970  0.020  1.090
 PH9  CC4  HC42  single    0.970  0.020  1.090
 PH9  CC3  CC6   single    2.929  0.020  2.929
 PH9  CC3  CC9   single    1.529  0.020  1.529
 PH9  CC3  HC3   single    0.970  0.020  1.090
 PH9  CC5  CC2   single    2.923  0.020  2.923
 PH9  CC5  C10   single    1.531  0.020  1.531
 PH9  CC5  HC5   single    0.970  0.020  1.090
 PH9  CC2  CC1   single    1.535  0.020  1.535
 PH9  CC2  HC21  single    0.970  0.020  1.090
 PH9  CC2  HC22  single    0.970  0.020  1.090
 PH9  CC6  CC1   single    1.542  0.020  1.542
 PH9  CC6  HC61  single    0.970  0.020  1.090
 PH9  CC6  HC62  single    0.970  0.020  1.090
 PH9  CC1  CC7   single    1.541  0.020  1.541
 PH9  C10  CC8   single    1.531  0.020  1.531
 PH9  C10  H101  single    0.970  0.020  1.090
 PH9  C10  H102  single    0.970  0.020  1.090
 PH9  CC8  CC9   single    1.529  0.020  1.529
 PH9  CC8  CC7   single    1.531  0.020  1.531
 PH9  CC8  HC8   single    0.970  0.020  1.090
 PH9  CC9  HC91  single    0.970  0.020  1.090
 PH9  CC9  HC92  single    0.970  0.020  1.090
 PH9  CC7  HC71  single    0.970  0.020  1.090
 PH9  CC7  HC72  single    0.970  0.020  1.090

loop_
_chem_comp_angle.comp_id
_chem_comp_angle.atom_id_1
_chem_comp_angle.atom_id_2
_chem_comp_angle.atom_id_3
_chem_comp_angle.value_angle
_chem_comp_angle.value_angle_esd
 PH9  C1    CB2  CB1   121.69  3.000
 PH9  C1    CB2  CB3   120.34  3.000
 PH9  CB1   CB2  CB3   117.97  3.000
 PH9  HB3   CB3  CB4   118.86  3.000
 PH9  HB3   CB3  CB2   119.61  3.000
 PH9  CB4   CB3  CB2   121.52  3.000
 PH9  HB4   CB4  CB6   120.16  3.000
 PH9  HB4   CB4  CB3   120.52  3.000
 PH9  CB6   CB4  CB3   119.33  3.000
 PH9  OAB   CB6  CB5   122.20  3.000
 PH9  OAB   CB6  CB4   117.36  3.000
 PH9  CB5   CB6  CB4   120.40  3.000
 PH9  HB5   CB5  CB1   119.62  3.000
 PH9  HB5   CB5  CB6   121.01  3.000
 PH9  CB1   CB5  CB6   119.37  3.000
 PH9  HB1   CB1  CB5   118.32  3.000
 PH9  HB1   CB1  CB2   120.27  3.000
 PH9  CB5   CB1  CB2   121.41  3.000
 PH9  H2    C2   CO2   107.35  3.000
 PH9  H2    C2   N     107.58  3.000
 PH9  CO2   C2   N     110.81  3.000
 PH9  H2    C2   C1    108.77  3.000
 PH9  CO2   C2   C1    110.58  3.000
 PH9  N     C2   C1    111.59  3.000
 PH9  H12   C1   H11   106.65  3.000
 PH9  H12   C1   C2    108.65  3.000
 PH9  H11   C1   C2    109.66  3.000
 PH9  H12   C1   CB2   110.42  3.000
 PH9  H11   C1   CB2   108.99  3.000
 PH9  C2    C1   CB2   112.32  3.000
 PH9  HN    N    C     118.84  3.000
 PH9  HN    N    C2    117.04  3.000
 PH9  C     N    C2    123.17  3.000
 PH9  CC1   C    O     122.63  3.000
 PH9  CC1   C    N     115.51  3.000
 PH9  O     C    N     121.86  3.000
 PH9  OC2   CO2  OC1   123.97  3.000
 PH9  OC2   CO2  C2    124.80  3.000
 PH9  OC1   CO2  C2    111.22  3.000
 PH9  HC1   OC1  CO2   110.20  3.000
 PH9  CA1   OAB  CB6   118.79  3.000
 PH9  CA6   CA1  CA2   119.43  3.000
 PH9  CA6   CA1  OAB   121.30  3.000
 PH9  CA2   CA1  OAB   119.23  3.000
 PH9  BRA2  CA2  CA3   120.10  3.000
 PH9  BRA2  CA2  CA1   119.37  3.000
 PH9  CA3   CA2  CA1   120.53  3.000
 PH9  HA3   CA3  CA4   120.05  3.000
 PH9  HA3   CA3  CA2   120.29  3.000
 PH9  CA4   CA3  CA2   119.65  3.000
 PH9  HA4   CA4  CA5   120.41  3.000
 PH9  HA4   CA4  CA3   119.54  3.000
 PH9  CA5   CA4  CA3   120.05  3.000
 PH9  HA5   CA5  CA6   119.63  3.000
 PH9  HA5   CA5  CA4   120.19  3.000
 PH9  CA6   CA5  CA4   120.18  3.000
 PH9  HA6   CA6  CA5   120.53  3.000
 PH9  HA6   CA6  CA1   119.32  3.000
 PH9  CA5   CA6  CA1   120.15  3.000
 PH9  HC42  CC4  HC41  106.52  3.000
 PH9  HC42  CC4  CC5   110.31  3.000
 PH9  HC41  CC4  CC5   110.36  3.000
 PH9  HC42  CC4  CC3   109.91  3.000
 PH9  HC41  CC4  CC3   110.45  3.000
 PH9  CC5   CC4  CC3   109.26  3.000
 PH9  HC3   CC3  CC9   109.64  3.000
 PH9  HC3   CC3  CC6   150.18  3.000
 PH9  CC9   CC3  CC6   100.17  3.000
 PH9  HC3   CC3  CC4   109.61  3.000
 PH9  CC9   CC3  CC4   109.64  3.000
 PH9  CC6   CC3  CC4    58.67  3.000
 PH9  HC5   CC5  C10   109.62  3.000
 PH9  HC5   CC5  CC2   150.32  3.000
 PH9  C10   CC5  CC2   100.05  3.000
 PH9  HC5   CC5  CC4   109.84  3.000
 PH9  C10   CC5  CC4   109.47  3.000
 PH9  CC2   CC5  CC4    58.64  3.000
 PH9  HC22  CC2  HC21  107.03  3.000
 PH9  HC22  CC2  CC1   110.19  3.000
 PH9  HC21  CC2  CC1   109.87  3.000
 PH9  HC22  CC2  CC5   152.42  3.000
 PH9  HC21  CC2  CC5   100.54  3.000
 PH9  CC1   CC2  CC5    59.45  3.000
 PH9  HC62  CC6  HC61  106.11  3.000
 PH9  HC62  CC6  CC1   109.46  3.000
 PH9  HC61  CC6  CC1   111.20  3.000
 PH9  HC62  CC6  CC3   101.66  3.000
 PH9  HC61  CC6  CC3   152.20  3.000
 PH9  CC1   CC6  CC3    59.14  3.000
 PH9  CC7   CC1  CC6   108.79  3.000
 PH9  CC7   CC1  CC2   108.94  3.000
 PH9  CC6   CC1  CC2   108.41  3.000
 PH9  CC7   CC1  C     111.31  3.000
 PH9  CC6   CC1  C     109.43  3.000
 PH9  CC2   CC1  C     109.91  3.000
 PH9  H102  C10  H101  106.80  3.000
 PH9  H102  C10  CC8   110.34  3.000
 PH9  H101  C10  CC8   109.96  3.000
 PH9  H102  C10  CC5   110.15  3.000
 PH9  H101  C10  CC5   110.03  3.000
 PH9  CC8   C10  CC5   109.53  3.000
 PH9  HC8   CC8  CC7   108.71  3.000
 PH9  HC8   CC8  CC9   109.79  3.000
 PH9  CC7   CC8  CC9   109.61  3.000
 PH9  HC8   CC8  C10   109.74  3.000
 PH9  CC7   CC8  C10   109.58  3.000
 PH9  CC9   CC8  C10   109.40  3.000
 PH9  HC92  CC9  HC91  106.94  3.000
 PH9  HC92  CC9  CC8   110.14  3.000
 PH9  HC91  CC9  CC8   110.16  3.000
 PH9  HC92  CC9  CC3   110.25  3.000
 PH9  HC91  CC9  CC3   109.96  3.000
 PH9  CC8   CC9  CC3   109.35  3.000
 PH9  HC72  CC7  HC71  106.68  3.000
 PH9  HC72  CC7  CC8   110.18  3.000
 PH9  HC71  CC7  CC8   109.10  3.000
 PH9  HC72  CC7  CC1   109.89  3.000
 PH9  HC71  CC7  CC1   111.02  3.000
 PH9  CC8   CC7  CC1   109.92  3.000

loop_
_chem_comp_tor.comp_id
_chem_comp_tor.id
_chem_comp_tor.atom_id_1
_chem_comp_tor.atom_id_2
_chem_comp_tor.atom_id_3
_chem_comp_tor.atom_id_4
_chem_comp_tor.value_angle
_chem_comp_tor.value_angle_esd
_chem_comp_tor.period
 PH9  CONST_01  CB6   CB4  CB3  CB2     0.00   0.0  0
 PH9  CONST_02  CB6   CB5  CB1  CB2     0.00   0.0  0
 PH9  CONST_03  CB5   CB1  CB2  CB3     0.00   0.0  0
 PH9  CONST_04  CB5   CB6  CB4  CB3     0.00   0.0  0
 PH9  CONST_05  CB1   CB2  CB3  CB4     0.00   0.0  0
 PH9  CONST_06  CB1   CB5  CB6  CB4     0.00   0.0  0
 PH9  CONST_07  CA4   CA3  CA2  CA1     0.00   0.0  0
 PH9  CONST_08  CA4   CA5  CA6  CA1     0.00   0.0  0
 PH9  CONST_09  CA5   CA6  CA1  CA2     0.00   0.0  0
 PH9  CONST_10  CA5   CA4  CA3  CA2     0.00   0.0  0
 PH9  CONST_11  CA6   CA1  CA2  CA3     0.00   0.0  0
 PH9  CONST_12  CA6   CA5  CA4  CA3     0.00   0.0  0
 PH9  CONST_13  OAB   CB6  CB4  CB3   180.00   0.0  0
 PH9  CONST_14  C1    CB2  CB3  CB4   180.00   0.0  0
 PH9  CONST_15  C1    CB2  CB1  CB5   180.00   0.0  0
 PH9  CONST_16  OAB   CB6  CB5  CB1   180.00   0.0  0
 PH9  CONST_17  CA3   CA2  CA1  OAB   180.00   0.0  0
 PH9  CONST_18  CA5   CA6  CA1  OAB   180.00   0.0  0
 PH9  CONST_19  BRA2  CA2  CA3  CA4   180.00   0.0  0
 PH9  CONST_20  BRA2  CA2  CA1  CA6   180.00   0.0  0
 PH9  CONST_21  HB4   CB4  CB3  CB2   180.00   0.0  0
 PH9  CONST_22  HB5   CB5  CB1  CB2   180.00   0.0  0
 PH9  CONST_23  HB1   CB1  CB2  CB3   180.00   0.0  0
 PH9  CONST_24  HB3   CB3  CB4  CB6   180.00   0.0  0
 PH9  CONST_25  HA3   CA3  CA2  CA1   180.00   0.0  0
 PH9  CONST_26  HA5   CA5  CA6  CA1   180.00   0.0  0
 PH9  CONST_27  HA6   CA6  CA1  CA2   180.00   0.0  0
 PH9  CONST_28  HA4   CA4  CA3  CA2   180.00   0.0  0
 PH9  CONST_29  CC1   C    N    C2    180.00   0.0  0
 PH9  CONST_30  HN    N    C    CC1     0.00   0.0  0
 PH9  CONST_31  O     C    N    C2      0.00   0.0  0
 PH9  CONST_32  HC1   OC1  CO2  C2    180.00   0.0  0
 PH9  Var_01    CA2   CA1  OAB  CB6   123.89  30.0  2
 PH9  Var_02    C2    C1   CB2  CB3  -125.59  30.0  2

loop_
_chem_comp_chir.comp_id
_chem_comp_chir.id
_chem_comp_chir.atom_id_centre
_chem_comp_chir.atom_id_1
_chem_comp_chir.atom_id_2
_chem_comp_chir.atom_id_3
_chem_comp_chir.volume_sign
 PH9  chir_01  C2   C1   N    CO2  negativ
 PH9  chir_02  CC3  CC4  CC6  CC9  positiv
 PH9  chir_03  CC5  C10  CC2  CC4  positiv
 PH9  chir_04  CC1  CC6  CC2  C    positiv
 PH9  chir_05  CC8  C10  CC9  CC7  positiv

loop_
_chem_comp_plane_atom.comp_id
_chem_comp_plane_atom.plane_id
_chem_comp_plane_atom.atom_id
_chem_comp_plane_atom.dist_esd
 PH9  plan-1  CB2   0.020
 PH9  plan-1  CB3   0.020
 PH9  plan-1  CB4   0.020
 PH9  plan-1  CB6   0.020
 PH9  plan-1  CB5   0.020
 PH9  plan-1  CB1   0.020
 PH9  plan-1  C1    0.020
 PH9  plan-1  OAB   0.020
 PH9  plan-1  HB3   0.020
 PH9  plan-1  HB4   0.020
 PH9  plan-1  HB5   0.020
 PH9  plan-1  HB1   0.020
 PH9  plan-2  OAB   0.020
 PH9  plan-2  CA1   0.020
 PH9  plan-2  CA2   0.020
 PH9  plan-2  CA3   0.020
 PH9  plan-2  CA4   0.020
 PH9  plan-2  CA5   0.020
 PH9  plan-2  CA6   0.020
 PH9  plan-2  BRA2  0.020
 PH9  plan-2  HA3   0.020
 PH9  plan-2  HA4   0.020
 PH9  plan-2  HA5   0.020
 PH9  plan-2  HA6   0.020
 PH9  plan-3  C2    0.020
 PH9  plan-3  N     0.020
 PH9  plan-3  C     0.020
 PH9  plan-3  O     0.020
 PH9  plan-3  CC1   0.020
 PH9  plan-3  HN    0.020
 PH9  plan-4  C2    0.020
 PH9  plan-4  CO2   0.020
 PH9  plan-4  OC1   0.020
 PH9  plan-4  OC2   0.020
 PH9  plan-4  HC1   0.020

